-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_8205429-8404826

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GeneMark_model.83073_t
Valid prediction for GeneMark_model.83076_t
Valid prediction for GeneMark_model.83095_t
Valid prediction for GlimmerHMM_glimmerT_47605-T1
Valid prediction for snap_scaffold_20-snap.1832-T1
Valid prediction for Augustus_model.g31754.t1
Valid prediction for Augustus_model.g31753.t1
Valid prediction for GeneMark_model.83079_t
Valid prediction for snap_scaffold_20-snap.1837-T1
Valid prediction for snap_scaffold_20-snap.1827-T1
Couldn't classify 50968, 51020
Sorry, prediction pasa_asmbl_25910.p1 fails validation.
(GAA)	 AG	50968-51020	GT	AAG
(CCT)	 AG	51999-52431	GA	GAG
-recovered pasa_asmbl_25910.p1, terminal, 51999, 52431
-recovered pasa_asmbl_25910.p1, internal, 50968, 51020
Couldn't classify 174624, 174656
Couldn't classify 175472, 175675
Sorry, prediction pasa_asmbl_26392.p2 fails validation.
(TGG)	 TA	174624-174656	GT	CAG
(TTC)	 AG	174862-174948	GT	AGG
(CGC)	 AG	175472-175675	GG	GGG
-recovered pasa_asmbl_26392.p2, internal, 174862, 174948
Valid prediction for CodingQuarry_transcript_30517-T1
Valid prediction for snap_scaffold_20-snap.1824-T1
Valid prediction for GeneMark_model.83083_t
Valid prediction for GlimmerHMM_glimmerT_47588-T1
Valid prediction for GeneMark_model.83070_t
Valid prediction for GlimmerHMM_glimmerT_47604-T1
Valid prediction for pasa_asmbl_25917.p1
Valid prediction for GlimmerHMM_glimmerT_47589-T1
Valid prediction for Augustus_model.g31737.t1
Couldn't classify 46241, 46276
Couldn't classify 49038, 49191
Sorry, prediction pasa_asmbl_26294.p1 fails validation.
(CAT)	 AT	46241-46276	GT	AGG
(AAA)	 AG	46601-46717	GT	AGG
(ATA)	 AG	46840-46937	GT	CCG
(AAT)	 AG	47034-47142	GT	AGG
(GCC)	 AG	47256-47334	GT	CTG
(CCT)	 AG	47531-47661	GT	GGG
(CTC)	 AG	48082-48156	GT	AGG
(CTG)	 AG	48591-48802	GT	AAG
(GAA)	 AG	49038-49191	AG	CCA
-recovered pasa_asmbl_26294.p1, internal, 46601, 46717
-recovered pasa_asmbl_26294.p1, internal, 46840, 46937
-recovered pasa_asmbl_26294.p1, internal, 47034, 47142
-recovered pasa_asmbl_26294.p1, internal, 47256, 47334
-recovered pasa_asmbl_26294.p1, internal, 47531, 47661
-recovered pasa_asmbl_26294.p1, internal, 48082, 48156
-recovered pasa_asmbl_26294.p1, internal, 48591, 48802
Valid prediction for CodingQuarry_transcript_30518-T1
Valid prediction for GeneMark_model.83075_t
Valid prediction for Augustus_model.g31745.t1
Valid prediction for GlimmerHMM_glimmerT_47582-T1
Valid prediction for HiQ_model.g31743.t1
Valid prediction for Augustus_model.g31739.t1
Couldn't classify 59289, 59429
Sorry, prediction pasa_asmbl_25912.p1 fails validation.
(AAC)	 TG	59289-59429	GT	AGG
(GAG)	 AG	59712-59873	GT	AGG
(GTG)	 AG	60126-60251	GT	AGG
(AAA)	 AG	60521-60807	GT	AGG
(CAG)	 AG	60990-61123	GT	AGG
(AGC)	 AG	61466-61569	AA	AGA
-recovered pasa_asmbl_25912.p1, terminal, 61466, 61569
-recovered pasa_asmbl_25912.p1, internal, 59712, 59873
-recovered pasa_asmbl_25912.p1, internal, 60126, 60251
-recovered pasa_asmbl_25912.p1, internal, 60521, 60807
-recovered pasa_asmbl_25912.p1, internal, 60990, 61123
Valid prediction for GlimmerHMM_glimmerT_47586-T1
Valid prediction for GlimmerHMM_glimmerT_47590-T1
Valid prediction for GeneMark_model.83072_t
Valid prediction for GlimmerHMM_glimmerT_47595-T1
Valid prediction for GlimmerHMM_glimmerT_47597-T1
Valid prediction for Augustus_model.g31738.t1
Couldn't classify 169227, 169781
Sorry, prediction pasa_asmbl_25927.p1 fails validation.
(CGC)	 AT	169227-169781	TG	AGT
Valid prediction for snap_scaffold_20-snap.1830-T1
Valid prediction for GlimmerHMM_glimmerT_47584-T1
Valid prediction for snap_scaffold_20-snap.1822-T1
Valid prediction for GeneMark_model.83093_t
Valid prediction for GeneMark_model.83062_t
Valid prediction for GeneMark_model.83094_t
Valid prediction for GlimmerHMM_glimmerT_47585-T1
Valid prediction for pasa_asmbl_25930.p1
Valid prediction for Augustus_model.g31736.t1
Valid prediction for GeneMark_model.83085_t
Valid prediction for CodingQuarry_transcript_30516-T1
Valid prediction for snap_scaffold_20-snap.1821-T1
Valid prediction for GlimmerHMM_glimmerT_47596-T1
Valid prediction for HiQ_model.g31741.t1
Valid prediction for GeneMark_model.83061_t
Valid prediction for pasa_asmbl_25913.p1
Valid prediction for snap_scaffold_20-snap.1825-T1
Valid prediction for GlimmerHMM_glimmerT_47592-T1
Couldn't classify 110719, 110883
Sorry, prediction pasa_asmbl_25920.p1 fails validation.
(AGG)	 TA	110719-110883	GT	AGG
(ACA)	 AG	111842-112123	GT	AGG
(GAG)	 AG	113760-113885	GT	TAG
(GAG)	 AG	114294-114514	GT	AGG
(GCA)	 AG	116325-116554	GT	AGG
(AAC)	 AG	116675-116777	GT	GAG
(GAC)	 AG	117927-118140	CC	GAC
-recovered pasa_asmbl_25920.p1, terminal, 117927, 118140
-recovered pasa_asmbl_25920.p1, internal, 111842, 112123
-recovered pasa_asmbl_25920.p1, internal, 113760, 113885
-recovered pasa_asmbl_25920.p1, internal, 114294, 114514
-recovered pasa_asmbl_25920.p1, internal, 116325, 116554
-recovered pasa_asmbl_25920.p1, internal, 116675, 116777
Valid prediction for GeneMark_model.83065_t
Valid prediction for GlimmerHMM_glimmerT_47603-T1
Valid prediction for snap_scaffold_20-snap.1845-T1
Valid prediction for GeneMark_model.83082_t
Valid prediction for snap_scaffold_20-snap.1823-T1
Valid prediction for Augustus_model.g31740.t1
Valid prediction for GlimmerHMM_glimmerT_47593-T1
Valid prediction for GeneMark_model.83071_t
Valid prediction for snap_scaffold_20-snap.1828-T1
Valid prediction for GeneMark_model.83090_t
Valid prediction for HiQ_model.g31746.t1
Valid prediction for snap_scaffold_20-snap.1846-T1
Valid prediction for snap_scaffold_20-snap.1833-T1
Valid prediction for snap_scaffold_20-snap.1847-T1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for snap_scaffold_20-snap.1838-T1
Valid prediction for snap_scaffold_20-snap.1842-T1
Valid prediction for snap_scaffold_20-snap.1841-T1
Valid prediction for snap_scaffold_20-snap.1849-T1
Valid prediction for GlimmerHMM_glimmerT_47601-T1
Valid prediction for GeneMark_model.83086_t
Valid prediction for GeneMark_model.83067_t
Valid prediction for GlimmerHMM_glimmerT_47580-T1
Valid prediction for snap_scaffold_20-snap.1844-T1
Couldn't classify 101896, 102348
Sorry, prediction pasa_asmbl_26899.p1 fails validation.
(AAT)	 TC	101896-102348	GT	AGG
(ATC)	 AG	102720-102802	GT	AAG
(GTA)	 AG	103077-103233	GT	AGG
(GAG)	 AG	103733-103897	GT	AGG
(TTT)	 AG	104150-104275	GT	TGG
(AGA)	 AG	104704-104924	GT	AGG
(CCA)	 AG	105124-105161	GT	ACG
(AGG)	 AG	105394-105500	AC	AGA
add_exon() Sorry, pasa_asmbl_26899.p1 104704-104924-terminal-2 is invalid.
-recovered pasa_asmbl_26899.p1, terminal, 104704, 104924
-recovered pasa_asmbl_26899.p1, terminal, 105394, 105500
-recovered pasa_asmbl_26899.p1, internal, 102720, 102802
-recovered pasa_asmbl_26899.p1, internal, 103077, 103233
-recovered pasa_asmbl_26899.p1, internal, 103733, 103897
-recovered pasa_asmbl_26899.p1, internal, 104150, 104275
-recovered pasa_asmbl_26899.p1, internal, 104704, 104924
-recovered pasa_asmbl_26899.p1, internal, 105124, 105161
Valid prediction for Augustus_model.g31750.t1
Valid prediction for GeneMark_model.83080_t
Valid prediction for snap_scaffold_20-snap.1848-T1
Valid prediction for snap_scaffold_20-snap.1818-T1
Valid prediction for HiQ_model.g31749.t1
Valid prediction for GlimmerHMM_glimmerT_47598-T1
Valid prediction for GeneMark_model.83096_t
Valid prediction for GeneMark_model.83064_t
Valid prediction for GeneMark_model.83091_t
Valid prediction for GeneMark_model.83077_t
Valid prediction for GeneMark_model.83063_t
Valid prediction for GlimmerHMM_glimmerT_47591-T1
Couldn't classify 2426, 2591
Couldn't classify 3853, 3965
Sorry, prediction pasa_asmbl_26917.p1 fails validation.
(TTT)	 GT	2426-2591	GT	AGG
(ACA)	 AG	3610-3747	GT	GTG
(GGT)	 AG	3853-3965	CA	GAC
-recovered pasa_asmbl_26917.p1, internal, 3610, 3747
Couldn't classify 7897, 8039
Couldn't classify 8585, 8628
Sorry, prediction pasa_asmbl_26916.p1 fails validation.
(AAA)	 AA	7897-8039	GT	AAG
(CTT)	 AG	8132-8268	GT	AGG
(CTA)	 AG	8585-8628	AG	AGA
-recovered pasa_asmbl_26916.p1, internal, 8132, 8268
Valid prediction for snap_scaffold_20-snap.1829-T1
Valid prediction for snap_scaffold_20-snap.1840-T1
Couldn't classify 9580, 9594
Sorry, prediction pasa_asmbl_26915.p1 fails validation.
(CTT)	 CT	9580-9594	GT	TGG
(GAA)	 AG	10058-10203	GT	GGG
(TTC)	 AG	10332-10450	GT	AGG
(GTG)	 AG	11033-11157	GT	TGG
(CGT)	 AG	11293-11390	GT	AAG
(CAC)	 AG	11792-11919	GT	GAG
(CTT)	 AG	12291-12415	GT	GTG
(GTG)	 AG	12849-12994	GT	AGG
(CGT)	 AG	13191-13293	GT	AGG
(AAA)	 AG	13532-13674	GC	ACG
(GGA)	 AG	13904-14012	AC	GAA
add_exon() Sorry, pasa_asmbl_26915.p1 11792-11919-terminal-2 is invalid.
-recovered pasa_asmbl_26915.p1, terminal, 11792, 11919
-recovered pasa_asmbl_26915.p1, terminal, 13904, 14012
-recovered pasa_asmbl_26915.p1, internal, 10058, 10203
-recovered pasa_asmbl_26915.p1, internal, 10332, 10450
-recovered pasa_asmbl_26915.p1, internal, 11033, 11157
-recovered pasa_asmbl_26915.p1, internal, 11293, 11390
-recovered pasa_asmbl_26915.p1, internal, 11792, 11919
-recovered pasa_asmbl_26915.p1, internal, 12291, 12415
-recovered pasa_asmbl_26915.p1, internal, 12849, 12994
-recovered pasa_asmbl_26915.p1, internal, 13191, 13293
-recovered pasa_asmbl_26915.p1, internal, 13532, 13674
Valid prediction for GlimmerHMM_glimmerT_47581-T1
Couldn't classify 194103, 194201
Sorry, prediction pasa_asmbl_26897.p1 fails validation.
(CCG)	 AC	194103-194201	GT	AGG
(GCT)	 AG	194448-194600	GT	AGG
(GAT)	 AG	194870-194989	GT	AGG
(CTG)	 AG	195164-195314	GT	TGG
(CCA)	 AG	195586-195707	GT	TGG
(GCC)	 AG	196025-196067	GT	CGG
(AGC)	 AG	196222-196385	GA	AGG
-recovered pasa_asmbl_26897.p1, terminal, 196222, 196385
-recovered pasa_asmbl_26897.p1, internal, 194448, 194600
-recovered pasa_asmbl_26897.p1, internal, 194870, 194989
-recovered pasa_asmbl_26897.p1, internal, 195164, 195314
-recovered pasa_asmbl_26897.p1, internal, 195586, 195707
-recovered pasa_asmbl_26897.p1, internal, 196025, 196067
Valid prediction for Augustus_model.g31752.t1
Valid prediction for snap_scaffold_20-snap.1831-T1
Valid prediction for snap_scaffold_20-snap.1843-T1
Valid prediction for snap_scaffold_20-snap.1820-T1
Valid prediction for GeneMark_model.83060_t
Couldn't classify 51151, 51315
Sorry, prediction pasa_asmbl_26911.p2 fails validation.
(GCC)	 CA	51151-51315	GT	TGG
(GCT)	 AG	51678-51803	GT	AGG
(TGC)	 AG	52973-53110	GG	GAG
-recovered pasa_asmbl_26911.p2, terminal, 52973, 53110
-recovered pasa_asmbl_26911.p2, internal, 51678, 51803
Valid prediction for GeneMark_model.83074_t
Valid prediction for GlimmerHMM_glimmerT_47594-T1
Valid prediction for GlimmerHMM_glimmerT_47587-T1
Valid prediction for GeneMark_model.83092_t
Valid prediction for snap_scaffold_20-snap.1839-T1
Valid prediction for GeneMark_model.83068_t
Valid prediction for GeneMark_model.83089_t
Valid prediction for GlimmerHMM_glimmerT_47583-T1
Valid prediction for GeneMark_model.83088_t
Valid prediction for HiQ_model.g31744.t1
Couldn't classify 61022, 61111
Sorry, prediction pasa_asmbl_26901.p1 fails validation.
(CCT)	 CT	61022-61111	GT	CGG
(AAT)	 AG	61987-62067	GT	AGG
(GTT)	 AG	62467-62598	GT	AGG
(ATT)	 AG	62850-63021	GT	CGG
(ATT)	 AG	64205-64377	GT	AGG
(AGG)	 AG	64697-64798	GT	GGG
(CTG)	 AG	65249-65510	GT	CGG
(AAA)	 AG	65688-65905	TC	GAT
-recovered pasa_asmbl_26901.p1, terminal, 65688, 65905
-recovered pasa_asmbl_26901.p1, internal, 61987, 62067
-recovered pasa_asmbl_26901.p1, internal, 62467, 62598
-recovered pasa_asmbl_26901.p1, internal, 62850, 63021
-recovered pasa_asmbl_26901.p1, internal, 64205, 64377
-recovered pasa_asmbl_26901.p1, internal, 64697, 64798
-recovered pasa_asmbl_26901.p1, internal, 65249, 65510
Valid prediction for Augustus_model.g31748.t1
Valid prediction for Augustus_model.g31747.t1
Valid prediction for snap_scaffold_20-snap.1834-T1
Valid prediction for GlimmerHMM_glimmerT_47600-T1
Valid prediction for snap_scaffold_20-snap.1835-T1
Valid prediction for GlimmerHMM_glimmerT_47606-T1
Valid prediction for GeneMark_model.83081_t
Valid prediction for Augustus_model.g31755.t1
Valid prediction for HiQ_model.g31735.t1
Valid prediction for GeneMark_model.83084_t
Valid prediction for Augustus_model.g31751.t1
Valid prediction for snap_scaffold_20-snap.1836-T1
Valid prediction for CodingQuarry_transcript_30519-T1
Valid prediction for GlimmerHMM_glimmerT_47599-T1
Valid prediction for snap_scaffold_20-snap.1819-T1
Valid prediction for GeneMark_model.83069_t
Valid prediction for GeneMark_model.83066_t
Couldn't classify 42997, 43365
Sorry, prediction pasa_asmbl_26913.p1 fails validation.
(ATG)	 TC	42997-43365	GG	CAG
Valid prediction for GeneMark_model.83078_t
Valid prediction for Augustus_model.g31742.t1
Valid prediction for snap_scaffold_20-snap.1826-T1
Valid prediction for GlimmerHMM_glimmerT_47602-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 85424, rend_intergenic: 82884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95285, rend_intergenic: 93899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112235, rend_intergenic: 107546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118140, rend_intergenic: 113163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159728, rend_intergenic: 154771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199398
-exon list size: 497


building trellis

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74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 85424, rend_intergenic: 82884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95285, rend_intergenic: 93899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112235, rend_intergenic: 107546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118140, rend_intergenic: 113163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159728, rend_intergenic: 154771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support